OK, I know I'm raising a thread from the dead, but this is an issue I was dealing with, and was able to solve. I thought the issue was the seat as well, but couldn't figure out why it would cause me any problem.
The Issue:
The pedal is located VERY close to the right side of the driver's footwell. This means that you can either:
1) Drive with your foot on the pedal, oriented more or less vertically. You will have to hold your leg up, or twist your leg and ankle at a funny angle.
2) Drive with your heel in front of the brake pedal, and your foot turned at a far rightward list, pushing on the accelerator with your toe. This will put your knee against the edge of the shifter - Annoying in an automatic, bad juju if you row your own.
Either way, it's going to make your thigh uncomfortable. If you hold your leg up, you'll feel that you need more thigh support to hold it up. If you twist your foot and lean your knee out over the console, you'll feel that the seat isn't large enough to support your leg.
So, I did what anyone with a nicely sharpened Swiss Army Knife would do: I pulled the carpeting up, tried to cut it, and gave up and got some real scissors. I cut out the thick chunk of sound-deadening material that was behind the vertical surface of carpet to the right of the pedal. Just ripped it out.
Once I pushed the carpet back down and settled it into place, Voila! I can now have my foot solidly on the pedal, with a bit of extra space to the right side. If it makes a bit of extra interior noise, I'll turn up the radio.
As you can see, the noise-deadening material is pretty thick. It looks like Honda must've been collecting laundry lint from its employees to recycle into filler.
If anyone else is having this issue, this was a good solution for me.